Salmonella Thompson, a notable foodborne pathogen, is seldom identified as pathogenic in poultry. Unexpectedly, S. Thompson was detected as a pathogen in white-feather broiler embryos at a poultry facility in China. Hence, this research aimed to investigate the antimicrobial resistance and pathogenic traits of clinical S. Thompson isolates from deceased poultry embryos. Phylogenetic analysis based on 16S rRNA and seven housekeeping genes indicated that the 14 clinical S. Thompson isolates were genetically close. Core-genome multilocus sequence typing (cgMLST) of these isolates, derived from whole-genome sequencing, classified them as cgST-12774—identical to the two S. Thompson human strains previously reported in China (NCBI database). Antimicrobial resistance gene profiling revealed that all isolates carried aac(6′)-Iaa and the polymyxin resistance gene mcr-9. Susceptibility testing against 18 antibiotics showed resistance to streptomycin (100%), ampicillin (35.7%), and doxycycline (14.3%), while maintaining sensitivity to polymyxin B, confirming that mcr-9 did not exhibit a resistance phenotype. Virulence gene screening identified Salmonella pathogenicity islands SPI1–SPI5, fimbrial gene fimA, flagellar genes (bcfC, flhD, fliA, fliC, fljB, flgK, lpfC), and other virulence-associated genes (iroN, pagC, cigR) in all isolates. Furthermore, yolk sac inoculation in 1-day-old chicks demonstrated that the clinical S. Thompson strain was highly virulent to neonates. This research emphasizes that S. Thompson isolated from poultry embryos and those causing human infections in parts of China share the same cgMLST type (cgST-12774), confirming the pathogenic potential of this strain in chicks.
